OK, the default AI is, as with lots of games.. meh. But it's not too awful; I can deal with only giving them things I don't mind them using, tweaking their AI slightly, and really i'm fine with "hey, a fight, i'ma go hit something" in most situations.
Every now and then, that is a problem; the bandit camp for instance, or other situations where I need to tell them to do things like "please don't run through that hall full of traps".

The problem is that as soon as I give a command for any reason, their previous intelligence (as it was) seems to be banished forever; they won't even defend themself anymore unless I command them all to turn into a band of fearless murder hobos. How do I get them back to their default behavior? I hate tactical RPGs, and I don't want to end up hating this game for turning into one when it wasn't before.

Personally I think their intelligence goes right out the window as soon as Artificial Idiocy is turned on, so I'm impressed you can play with that on. Not exactly sure what you mean here though. AI can be turned on or off with the button in the bottom left corner, or by choosing Puppet mode ON, in Character -> Behaviour. If you just give them individual commands while AI is on, I would think they should turn back to whatever their Behaviour settings are after said enemy has been killed or spell cast. Not sure about that though, do they get 'stuck' somehow, so they just stand there with their tumbs up their bums?

I've just played an area where there were 200 thieves coming for us (felt like it anyway), and I don't want to think about what they would have done in that area with AI on. Thankfully cleave works with AI off, so the game plays much better for me now when I've gotten more used to the atrociously bad UI (and the likewise atrociously bad AI is killed).

Well, the thing is that bad AI evens out for most things, because the enemy is being just as stupid. The main issue is that sure, I can play in puppet mode; in that case, the game turns into a type of strategic game that I hate playing. Whereas if I just watch what the companions have like in Arcanum so that their bad decisions are still pretty decent, it plays fine for me.

Just telling them to "guard me" usually works for me.

What you do is just issue the Broadcast Command "Attack Nearest" This will reset the AI. This can be done anywhere in any situation.

...then watch your mage run all across the map to attack some schmuck, activating most of the enemies on the map to attack. Awesome AI.

Try TonyK;s Companion and Monster AI 2.2 to smarten up the AI
http://nwvault.ign.com/View.php?view=NWN2HakpaksOriginal.Detail&id=141